fMRIPrep fails during autorecon1 in multiple subjects

[Steven]

Hi @Dustin,

@Dustin

If I were to run FreeSurfer separately, would I need to reprocess all participants from scratch to maintain consistency?

That would be recommended.

@Dustin

I also have a related question: my participants have between 1 and 6 scanning sessions. I read that if there are two sessions, fMRIPrep uses both T1w images to build a robust template, but if there are more, only one is selected. Is that correct?

Not quite. From https://neurostars.org/t/what-does-fmriprep-do-with-t1w-with-longitudinal/21184:

@effigies

The --longitudinal flag tells fMRIPrep to try to find a template T1w image that is equidistant from all time points, rather than aligning to the first time point. This takes significantly longer, as it’s an iterative process, but I don’t have a sense of how it scales with number of time points.

@Dustin

If so, is there a good way to replicate this behavior in FreeSurfer…

See steps fro creating unbiased template in LongitudinalProcessing - Free Surfer Wiki.

@Dustin

, and then feed that output back into fMRIPrep?

Specify the --fs-subjects-dir, and if using the longitudinal freesurfer workflow, also specify --fs-no-resume.

@Dustin

I’ve tried running recon-all -all on both sessions independently and then using recon-all -base to create a subject template. Would this base template be compatible as input to fMRIPrep?

I think that would work, haven’t tried anything like that myself though.

Best,
Steven